Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
Basic information
species | Glycine max |
transcript | GLYMA04G09080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
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---------------gtaagttttctagttgttcgtcaatatattcttg--aatgttcatgt-----ttaattagctcagttaatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 5
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttc------agGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
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----------------------------gtgggcatcttttgactcttcctaat-taatcttgacagttcaat-gcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------gtgagtatctatctgaaa----tgatat-tgaaatgt-aatgcatcttatttttcttaatgtta--tagagaatattga--atagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
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gtaaacattcactctgagaaacatttactttattttgtagc-atctgaagattttgttatatgaaccattgataaacataatttttcctgagatgagcccttcaatattggtggcactcaccatatgatttgtgtgttttatacattccagGATGTCAACAGAGATGGTTGCATGCATTGCAATTGAGGCAATATCCATATTAGAAAAGATGCATTCTAGAGG
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttt---tatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
|||||| | ||||| || || | | || || | | |||| | ||| | | ||| || | | | | || ||| ||||| | ||||||||||||||| ||||| || || || || |||||||| ||||||||||| || |||||
gtgagtgagatgaaaatatgat-ttattattttttatatgctacaaatggttctgttgcttttaccattttgtgcttgtatttgcctaatgaagatatttgcttaattccagTATGTCCATTGAAATGGTTGCATGCATTGCTATTGAAGCAATATCCATATTGGAGAAGATGCACTCCAGAGG
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG----------------------------
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------------------------------------------------------gtaagtagctctttcgcctctctcgtcctaatctgccaatttttttaa----cagCATGTCTACTGAAATGGTTGCCTGTATTGCGGTGGAGGCTATTTCGATACTTGATAAAATGCATTCGCGGGGCTATGTTCACGGAGATGTGAAGCCAGAG
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG----------------------------
|| | | | | | || | || | | |||| ||| |||||||||||||||||||| |||||||| | |||||||| || ||| | || || |||||||| | ||
------------------------------------------------------gtaagtagctctttcgcctccctcgtcctaatctgccaatttttttaa----cagCATGTCTACTGAAATGGTTGCCTGTATTGCGGTGGAGGCTATTTCGATACTTGATAAAATGCATTCGCGGGGCTATGTTCACGGAGATGTGAAGCCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
agctaac putative branch site (score: 2)
cttttatttctttttc CT-rich tract
taacttttatttcttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG